The connectivity checker can be use to split a molecule by breaking bonds. We should document and test this use case more, one corner case not currently handled is the Sgroups. We need to check if a split molecule can inherit and Sgroup correctly.

Also an optimisation is to avoid the copy if there is only a single component. This is now super simple as the SDG seems to depend on some invariant that the molecule but not the atoms/bonds got copied so that needs to be investigated.

    public static IAtomContainerSet partitionIntoMolecules(IAtomContainer container) {
        ConnectedComponents cc = new ConnectedComponents(GraphUtil.toAdjList(container));
        if (cc.nComponents() == 1) {
            IAtomContainerSet acset = container.getBuilder().newInstance(IAtomContainerSet.class);
            acset.addAtomContainer(container);
            return acset;
        }
        return partitionIntoMolecules(container, cc.components());
    }